Question: How to create a simulated SNP genotypes dataset
0
gravatar for fairweath89
3.5 years ago by
United Kingdom
fairweath890 wrote:

I am trying to create a simulated SNP dataset, consisting of ~40 individuals from two populations, and data from around 1000 co-dominant SNP markers, exhibiting a predefined (low) level of structure. The result I am looking for is one similar to that given by genalex's create function, but the crucial difference is that I require a dataset comprising 4 SNP alleles overall (A,C,G,T), but only two alleles per SNP marker (A/T, C/G, C/T etc.). All combinations present, basically like you would expect from a typical population genetic SNP dataset. 

Essentially, I guess I am after a function that allows me to dictate parameters such as level of structure, no. of individuals, number of alleles overall and per SNP, and that delivers a SNP dataset that roughly adheres to those parameters. An R solution would be preferable as it is the only language I am comfortable with for the moment. 

snp R • 1.6k views
ADD COMMENTlink modified 3.5 years ago by andrew.j.skelton735.7k • written 3.5 years ago by fairweath890
2
gravatar for andrew.j.skelton73
3.5 years ago by
London
andrew.j.skelton735.7k wrote:

Plink is by far your best bet for this - http://pngu.mgh.harvard.edu/~purcell/plink/simulate.shtml 

ADD COMMENTlink written 3.5 years ago by andrew.j.skelton735.7k
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